[GSoC] GSoC Digest, Vol 25, Issue 3
victor.kofia at gmail.com
victor.kofia at gmail.com
Wed Jun 4 16:01:34 UTC 2014
Hello Everyone,
It just came to my attention that I haven’t been updating the OBF mailing list on my activities. My blog, located here (http://kofiav.blogspot.ca/), has a record of everything I’ve worked on so far. If anyone has questions on anything, don’t hesitate to leave a comment. Alternatively, you could also send me an email.
Thank you,
Victor
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Today's Topics:
1. Re: 3rd coding week blog post (Eric Talevich)
2. Re: JSBML Update-Ibrahim Vazirabad (Eric Talevich)
3. JSBML Update (Leandro Watanabe)
4. Re: JSBML Update-Ibrahim Vazirabad (Raoul Bonnal)
----------------------------------------------------------------------
Message: 1
Date: Tue, 3 Jun 2014 18:11:32 -0700
From: Eric Talevich <eric.talevich at gmail.com>
Subject: Re: [GSoC] 3rd coding week blog post
To: Sarah Berkemer <sarah.berkemer at gmail.com>
Cc: choener at tbi.univie.ac.at, OBF GSoC <gsoc at lists.open-bio.org>
Message-ID:
<CAMC681=YyKNKM8pC8wDR_6hdb_xj9dwtOQc19eMfn-vG-sAD0w at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
OK, makes sense. Do you have another public repository where your GSoC code
will be hosted? I'm not very familiar with Darcs, so I'm not sure whether
it makes more sense to have a branch for your work in Ketil's repo (like
SourceForge), or as a fork that you control entirely (like GitHub). Either
way, the goal is to ensure that your GSoC code is publicly available.
On Tue, Jun 3, 2014 at 4:23 AM, Sarah Berkemer <sarah.berkemer at gmail.com>
wrote:
> Hey,
>
> the code is written by Ketil Malde and can be downloaded here:
> http://malde.org/~ketil/biohaskell/transalign/ . I probably should
> include this into my blog.
> The 'transalign_prof' version is just the version where I put in some
> flags to get more detailed statistics. And yes, I did the plots with this
> program and the Haskell profiling library :) .
>
> Sarah
>
>
> On Mon, Jun 2, 2014 at 5:19 PM, Eric Talevich <eric.talevich at gmail.com>
> wrote:
>
>> Hi Sarah,
>>
>> This looks very cool so far. Can you point me to the source code for the
>> script transalign_prof, and was that the same program that generated
>> those nice plots on the wiki?
>>
>> Thanks,
>> Eric
>>
>>
>>
>>
>> On Mon, Jun 2, 2014 at 6:49 AM, Sarah Berkemer <sarah.berkemer at gmail.com>
>> wrote:
>>
>>> Hello,
>>>
>>> here is my blogpost and plan for the third coding week.
>>> In the last week, I did a time and space profiling analysis, showing
>>> which
>>> methods are the ones which have the most time and space consumption.
>>> Here http://biohaskell.org/GSoC_blog/Weeks_1and2 , you can find the
>>> results
>>> of the analysis, including plots.
>>> Now, I know which methods have to be changed. In this week I plan to
>>> fully
>>> understand those methods and think about whether to rewrite them or just
>>> change some parts. The plan for this week can be found here:
>>> http://biohaskell.org/GSoC_blog/Weeks_3and4 .
>>>
>>> Sarah
>>> _______________________________________________
>>> GSoC mailing list
>>> GSoC at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>>
>>
>>
>
------------------------------
Message: 2
Date: Tue, 3 Jun 2014 18:38:00 -0700
From: Eric Talevich <eric.talevich at gmail.com>
Subject: Re: [GSoC] JSBML Update-Ibrahim Vazirabad
To: Ibrahim Vazirabad <yvazirabad at gmail.com>
Cc: OBF GSoC <gsoc at lists.open-bio.org>
Message-ID:
<CAMC681mfmhA-VeUvXE1ayqETvOvA0ObDMVc0SPRJ50WAsx-4Zw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi Ibrahim,
Looks good so far. I see Team JSBML is working very efficiently :)
Do you have a public repository for you're developing, or a branch in the
main JSBML repo? I'd like to link to it from the OBF wiki.
Thanks,
Eric
On Mon, Jun 2, 2014 at 8:10 PM, Ibrahim Vazirabad <yvazirabad at gmail.com>
wrote:
> Hello all,
>
> I have a new blog post at my GSoC blog:
> http://jsbmlcelldesigner2014.blogspot.com/
>
> It mostly has to do with JUnit testing and architecture schematics to
> facilitate CellDesigner/JSBML data structure mapping.
>
> Respectfully,
> Ibrahim Vazirabad
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
>
------------------------------
Message: 3
Date: Tue, 3 Jun 2014 21:29:12 -0600
From: Leandro Watanabe <leandrohw at gmail.com>
Subject: [GSoC] JSBML Update
To: Eric Talevich <eric.talevich at gmail.com>
Cc: OBF GSoC <gsoc at lists.open-bio.org>
Message-ID: <80E4CDA1-7A20-4486-9658-F9572FCE0D98 at gmail.com>
Content-Type: text/plain; charset=us-ascii
Hi everyone,
I am working on extending the math for the arrays package now. I have a new blog: http://lhwatanabe.blogspot.com/2014/06/weekly-log-may-26-june-1.html
I usually write every sunday or monday about what I worked on the previous week.
You can checkout the code I have worked on here: svn://svn.code.sf.net/p/jsbml/code/trunk/extensions/arrays/
I have made a few changes to JSBML core as well (to incorporate the necessary math).
Leandro
------------------------------
Message: 4
Date: Wed, 4 Jun 2014 11:04:50 +0200
From: Raoul Bonnal <bonnal at ingm.org>
Subject: Re: [GSoC] JSBML Update-Ibrahim Vazirabad
To: Eric Talevich <eric.talevich at gmail.com>
Cc: Ibrahim Vazirabad <yvazirabad at gmail.com>, OBF GSoC
<gsoc at lists.open-bio.org>
Message-ID: <ACFEB55B-F2EC-492B-9D91-ADD1DE0AAC53 at ingm.org>
Content-Type: text/plain; charset=windows-1252
Hi Ibrahim,
I was reading http://jsbmlcelldesigner2014.blogspot.it/2014/05/on-to-week-3.html
and I think that would be useful to other people if you expand a bit the ?how to? set up a development environment for JSBML.
Why not adding tags to the blog, like week1, week2,?, weekn.. milestones etc?
Btw nice work.
On Jun 4, 2014, at 3:38 AM, Eric Talevich <eric.talevich at gmail.com> wrote:
> Hi Ibrahim,
>
> Looks good so far. I see Team JSBML is working very efficiently :)
>
> Do you have a public repository for you're developing, or a branch in the
> main JSBML repo? I'd like to link to it from the OBF wiki.
>
> Thanks,
> Eric
>
>
>
> On Mon, Jun 2, 2014 at 8:10 PM, Ibrahim Vazirabad <yvazirabad at gmail.com>
> wrote:
>
>> Hello all,
>>
>> I have a new blog post at my GSoC blog:
>> http://jsbmlcelldesigner2014.blogspot.com/
>>
>> It mostly has to do with JUnit testing and architecture schematics to
>> facilitate CellDesigner/JSBML data structure mapping.
>>
>> Respectfully,
>> Ibrahim Vazirabad
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>
> _______________________________________________
> GSoC mailing list
> GSoC at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/gsoc
------------------------------
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